Organization processes of proteins in crowded cellular environments are a key to the understanding of information transduction between cells. The motion of proteins in cells is not a simple random walk between different proteins and ligands, leading to a dynamical organization of the cytosol. The characterization of cellular organization processes is difficult with current experimental techniques and state of the art computer simulations. The aim of this project is to develop a theory capable of describing the role of specific protein interactions, dynamics and the combined effect of low-affinity interactions in cellular organization. For this purpose, a new computer simulation strategy will be developed based on adjustable coarse grained modeling. The coarse grained simulation strategy will be applied in combination with atomistic simulations to study dynamical organization of calcium ions and calcium binding proteins in neurons.